Apparatus and method for integrating a physical molecular model with a computer-based visualization and simulation model

ABSTRACT

Modeling systems are enhanced by combining physical and virtual modeling techniques to create a hybrid modeling system. Manipulation of physical models results in updated real-time physical characteristics being provided to a virtual model. User manipulation of virtual model characteristics can also be provided and implemented on the physical model using actuators and control devices. The invention also enables multiple users to simultaneously construct and manipulate different portions of a physical model, e.g., of an atom or a molecule, and to have the results of these manipulations provided to a computer system for computational analysis. The results of such analyses can be electronically returned to the physical model, e.g., wirelessly.

RELATED APPLICATIONS

This application claims benefit of U.S. Provisional Patent ApplicationNo. 60/437,525, filed Dec. 31, 2002, and U.S. Provisional PatentApplication No. 60/477,283, filed Jun. 10, 2003.

FIELD OF INVENTION

The present invention relates generally to physical modeling andsimulation and, more particularly, to an apparatus and method forinterfacing a physical molecular model with a computer system formolecular visualization and simulation.

BACKGROUND

Molecular modeling generally consists of two fields: physical molecularmodeling tool kits and the resulting physical models, and computer-basedmolecular visualization and simulation software (i.e., virtualmodeling).

Physical modeling tool kits allow a person to build a physicalrepresentation, e.g., of the atomic structure of a molecule. Thesemolecular modeling tool kits consist of hardware elements, usuallyspherical, that represent individual atoms and other hardware elements,usually rod-shaped, that represent bonds between atoms. Molecularmodeling tool kit users can construct a physical model that demonstratesthe static properties of a particular molecular structure, such as theatomic structure and the distance between atoms.

Physical modeling tool kits such as these are static andnon-interactive. The resulting three-dimensional (“3-D”) physical modelcannot represent characteristics of the system that are not obvious tothe human eye, such as the energetics of the system. Further, suchmodels cannot represent the dynamic characteristics of the molecularsystem when it is in a changing environment such as shifting loads,stresses, or molecular and atomic interactions. Changing experimentalvariables also are not readily modeled, such as varying wind loads on atruss, bridge, or civil structure. Finally, molecular modeling tool kitsand physical models do not computationally process or represent avirtual model of the subject matter on a computer screen.

Virtual software tools allow a user to create a virtual model, e.g., amolecule on a computer, to visualize the atomic structure and tosimulate the characteristics of the molecular system. Examples of suchcommercially available software tools include Insight II, available fromAccelrys (www.accelrys.com), and Virtual Molecular Dynamics (Universityof Chicago). Some such software tools are capable of representing themolecular structure, analyzing the molecular energetics, and simulatingchanges within the molecule or interactions with other molecules. Somesoftware tools incorporate quantum mechanical effects, either bysemi-empirical methods or using actual ab initio methods.

Unfortunately, although state-of-the-art visualization and simulationsoftware is sufficiently powerful to simulate a molecular or otherstructure, it is difficult to obtain the geometry of choice bymanipulating a virtual model on the computer screen. The user inputinterface in both creating the virtual model or in modifying that modelfor simulation is generally limited to the keyboard/mouse or a similarhuman-computer interface. The user can control only one parameter at atime, such as the rotation of a dihedral angle or the addition of a newatom. This process is unintuitive and time consuming.

Rather, it is more intuitive and faster to manipulate by hand a physical3-D physical model, conforming it to the geometry of choice. However,such physical models are static and are not capable of simulatingcomplex characteristics of the resulting structure. Even after thepreferred geometry is obtained, only limited useful information can beobtained without a computer and the appropriate visualization andsimulation software.

What is needed is a modeling system that includes the benefits of bothphysical and virtual modeling systems. Such a hybrid modeling systemshould include the speed and ease-of-use characteristics of physicalmodels, and also include the advanced computational and visualizationtools available in computer-based virtual modeling programs.

SUMMARY OF THE INVENTION

The present invention seeks to overcome the limitations of physical andvirtual models described above by integrating them with each other.Aspects of the invention include physical models that communicate withcomputer-based visualization and simulation software tools, and virtualmodels that send information to physical models.

One aspect of the invention features a node element for use inassembling a plurality of structural elements, the node elementcomprising a body and one or more connection ports disposed relative tothe body. At least one of the connection ports can be coupled to anadjacent structural element. The node element also includes acomputational unit within the body, which receives information ofphysical characteristics of the node element from the connection port.The node element can also include a communications device capable ofproviding node element information, such as the information of thephysical characteristics. The information can be used to determine atopology of the node element. The information of physicalcharacteristics can be obtained from a sensor disposed within the nodeelement, e.g., at or near the connection port. The information ofphysical characteristics from the sensors can be received by thecomputational unit.

Different types of sensors can be used with the node element, includingsensors that detect information about at least one of movement of thenode element with respect to a bond element, rotational orientation withrespect to the connection port, movement of the node element withrespect to one of the structural elements, position or movement of thenode element with respect to an external spatial orientation referencepoint, and physical stress upon the node element. Sensors can includerotational sensors, accelerometers, a compass, an inclinometer,magnetometers, and gyroscopes. Some sensors can store or provideinformation relating to changes in the physical characteristics of thenode element.

Embodiments also include the adjacent structural element comprising abond element. Embodiments can also include a control device thatmanipulates a physical characteristic, e.g., the connection port. Thecontrol device can include an actuator, a vibrating unit, and/or a lightemitting diode.

The node element can include a communications device that transfers datafrom the computational unit to one of the structural elements. Acommunications device of a first node element can also transferinformation from a second computational unit disposed within a secondnode element to one of the structural elements, e.g., a structuralelement adjacent to the first node element. Data from a computationalunit, such as information of physical characteristics of the nodeelement, can be provided to a computer system external to the nodeelement or the plurality of structural elements. Such data can beexchanged in both directions using the communications device, betweenthe computational unit and the external computer system. Thecommunications device can include a wireless transmitter, and thewireless transmitter can be used for this purpose.

Some embodiments include a node element comprising a power transmissioninterface, which is capable of transferring power, e.g., from a sourceexternal to the node element through at least one of the connectionports to the node element.

Another aspect of the invention features a bond element for use inassembling a plurality of structural elements, comprising a body and afirst and second connection port disposed relative to the body. At leastone of the connection ports can be coupled to an adjacent structuralelement. A computational unit is disposed within the body and receivesinformation of physical characteristics of the bond element from thefirst or second connection ports. Sensors can be used to detect suchinformation, and suitable sensors include sensors that detectinformation about at least one of movement of the bond element withrespect to a structural element, rotational orientation with respect tothe connection port, position or movement of the bond element withrespect to an external spatial orientation reference point, and physicalstress upon the bond element. The sensors can include rotationalsensors, accelerometers, a compass, an inclinometer, magnetometers, andgyroscopes.

Yet another aspect of the invention is a hybrid modeling systemcomprising a physical model and a virtual model. The physical modelincludes at least one node element capable of being coupled to astructural element, the node element including information aboutphysical characteristics of the node element. The virtual model runs ona computer system and the information of the physical characteristics isprovided electronically from the physical model to the virtual model.The information of physical characteristics relates to a topology of thenode element, and can include information relating to other structuralelements of the model. The information of physical characteristics canbe provided by a sensor disposed within or connected to the nodeelement.

The modeling system can include a software program running on thecomputational unit and in communication with a software program runningon the computer system of the virtual model. The software program of thecomputer system can include a graphic display visualization unit, andthe visualization unit can present to a user a graphic displayrepresenting at least a portion of the physical model, at least aportion of the virtual model, or at least portions of both the physicaland virtual models. The visualization unit can display structureinformation, energetic information, and physical properties, e.g., fromthe physical or virtual model of the hybrid model.

Embodiments include a communications system that provides informationfrom the computer system of the virtual model to the computational unitof the physical model. Information can be provided to the node elementfrom the computer system that actuates a control device disposed withinor adjacent to the node element. The actuation of the control device cancorrespond to a virtual characteristic of the virtual model. Theinformation can be wirelessly communicated from the computer system.

Another aspect of the invention features a structural modeling kit foruse in assembling a plurality of structural elements, comprising atleast one bond element and at least one node element. The bond elementincludes a body and a first and second connection port disposed relativeto the body of the bond element. The node element includes a body and anode connection port disposed relative to the body of the node elementcapable of being coupled to the bond element, and a computational unitdisposed within the body of the node element. The computational unitreceives information of physical characteristics of the node elementfrom the node connection port.

Node elements and bond elements of the structural modeling kit can becoupled to correspond to at least a portion of a molecular model. Atleast one of the node element or the bond element includes acommunications device capable of providing the information of physicalcharacteristics to an external computer system.

Yet another aspect of the invention is a method of incorporatingphysical information into a virtual model which comprises the step ofproviding a modeling system that includes a physical model that includesat least one node element capable of being coupled to a structuralelement, the node element comprising a computational unit includinginformation of physical characteristics of the node element, and avirtual model that runs on a computer system. The information ofphysical characteristics is electronically provided from the physicalmodel to the virtual model.

BRIEF DESCRIPTION OF THE DRAWINGS

The foregoing discussion will be understood more readily from thefollowing detailed description of the invention, when taken inconjunction with the accompanying drawings, in which:

FIG. 1 is an exemplary diagram of an integrated physical model andsoftware system for assembling, visualizing and simulating a molecularstructure according to an embodiment of the present invention;

FIGS. 2A and 2B are exemplary diagrams illustrating the component partsof a molecular model comprising a node (which represents an atom) and abond (which represents a connection between two nodes);

FIGS. 3A and 3B are a exemplary diagrams of the elements of thecomponent parts of a molecular model;

FIGS. 4A and 4B are a exemplary diagrams of the construction of a simplemolecule model;

FIG. 5 is an exemplary diagram of a simple molecular model;

FIG. 6 is an exemplary diagram of a more complex molecular model; and

FIG. 7 illustrates some of the physical characteristics of a complexmolecular model.

DETAILED DESCRIPTION

Modeling systems are used to represent, simulate, and predict thereaction of various structures within and between themselves, andgenerally include the coupling together of a plurality of structuralelements. Such structural elements can include nodes and bonds. Bondsare commonly used to couple nodes together, and these can be used torepresent, for example, molecular and atomic particles and interactions.However, similar structural modeling elements are used in manytechnological fields, including buildings, bridges, trusses,foundations, and many other civil structures. The invention is useful inthese fields, as well as in the field of atomic and molecular modeling,and others. The invention encompasses both physical and computer-based(virtual) modeling systems. For clarity and ease of description, thefollowing discussion and explanations focus primarily on molecularmodeling technology. However, the invention has application to manyother, additional, fields of endeavor.

The figures and descriptions of the present invention have beensimplified to illustrate elements that are relevant for a clearunderstanding of the present invention while eliminating, for purposesof clarity, other elements. For example, certain system architecturedetails, such as certain details of the hardware and softwarecharacteristics, are not described herein. Those of ordinary skill inthe art will recognize, however, that these and other elements may bedesirable in a typical modeling kit, model, software system, orcommunications network. A discussion of such elements is not providedbecause such elements are known in the art and because they do notfacilitate a better understanding of the present invention.

The present invention enables a user or multiple users to construct andmanipulate a physical model of any molecule or molecular system and tohave these manipulations be transparently transferred to a computersystem for computational analysis. Different users can conveniently workon different portions of a physical model from different geographicallocations, and the cumulative results of their efforts can be combinedin a virtual model. Additionally, these users can simultaneously work ondifferent aspects of a hybrid physical/virtual model while the users arelocated in different locations. These benefits are particularly usefulfor very complex models.

A limitation of previous physical and virtual modeling tools (e.g., ofmolecular systems) is that there is no way to physically manipulate a3-D model in the user's hands and have those changes reflected on thecomputer, where more complicated molecular characteristics can beanalyzed. The present invention models and simulates any molecularsystem including, e.g., proteins, oligonucleotides, and otherbiomolecular systems, in both a physical representation and a virtualrepresentation.

FIG. 1 is an exemplary diagram hybrid modeling system that includes anintegrated physical model and software system for assembling,visualizing and simulating a molecular structure. The inventionovercomes the limitations of the prior art by interconnecting a physicalthree-dimensional molecular model 20, constructed from a hybrid modelingsystem tool kit, with a computer system, such as a computer 21 with adisplay screen. The computer interfaces with a molecular visualizationsoftware tool 22 and a molecular simulation software tool 23. Thesoftware tools are capable of representing characteristics of aparticular molecule and the changing characteristics of that molecule asit is subject to changing environments and changing molecularstructures. One embodiment is an energy calculation tool 24 that updatesthe energy characteristics of the molecular system as the physical modelis modified. Calculated variables can include Van der Walls energies,internal conformational energies (such as bonds angles, and dihedrals),screened Coulombic energies, solvation energies, and the like. Thus, thephysical model can be represented in a computer-based software toolwhere complex calculations can be performed to determine, e.g.,high-level quantum mechanical calculations, molecular dynamics, and manyother types of physical characteristics. Various rendering and moviemaking capabilities can also be included in the software running on thecomputer 21.

As discussed in more detail below, the physical model 20 can includeinformation of physical characteristics of the physical model, which canbe provided from the physical model 20 to the software (i.e., thevirtual model) running on the computer 21.

The physical model of the invention can be likened to an intelligent,inter-connected molecular LEGO® (Trademark of Interlego A.G.Corporation, Switzerland) set, except that molecular structures areconstructed rather than toy buildings or toy robots. A user can assemblea three-dimensional model representing a molecular structureatom-by-atom. Each atomic unit can have embedded knowledge of itself,i.e., of its own state, and knowledge of the existence (or absence) ofsingle or multiple neighboring or adjacent nodes or bonds. Some or allof these units can have a sensor and processing infrastructure that candetect and interface with other nodes or bonds, and a communicationinfrastructure that can detect and interface with virtual visualizationand simulation software tools. Such communication can be transmittedelectronically by wired, wireless, or other types of transmissionsystems.

The molecular modeling tool kit can also include several elements thatallow for physical assembly of a model, embedded intelligence in amolecular model, and communication between atomic and molecularelements, across molecular systems, and with a computer-based softwaresystem. Following is a description of such an embodiment.

FIGS. 2A and 2B illustrate the basic component parts of a molecularmodel. A node element 1 can represent an atomic unit, and can bespherically shaped. Particular node elements can differ in size, color,or other characteristics according to the atom represented by that nodeelement. The node element I can include one or more node connectionports 2. These can be physical connection points with other nodeelements, and can use bond elements 3. Particular node connection ports2 can differ in size, color, depth, and other characteristics accordingto the atom or atomic bond associated with a given node connection port.A bond element 3 can represent an atomic connection or bond, and isusually rod-shaped. A bond element will generally have at least twoconnection ports that can be coupled to an adjacent structural element(e.g., a node element or another bond element), but it may have morethan two connection ports. Bond elements can differ by size, color andother characteristics, e.g., according to the atomic bond represented bya given bond element. For example, a certain shape (e.g., square,octagonal, or triangular) can be used to differentiate a single, double,or triple bond, or a different length or color can be used todifferentiate an ionic bond from a covalent bond.

FIGS. 3A and 3B are exemplary diagrams of certain functional elementsand component parts of a physical model. The node connection port 2 canbe static, such as a simple hole drilled into the node element. Someembodiments include a sensor 4, a control device 5, and a communicationinterface 6. The sensor 4 can determine the presence (or not) of a bondelement 3. Many types of sensors and sensor functions can be used,including but not limited to movement, rotation, position, stress,dynamic rotation or movement, accelerometers (to measure acceleration),a compass, inclinometers, magnetometers, and/or gyroscopes. Thesesensors can be used to identify information of physical characteristicsof the node element, and this information can be used to determine thetopology (i.e., the connection configuration and physicalcharacteristics) of the node element. In some embodiments (not shown)two node elements can be coupled to each other without a bond element.Actuation of the control device 5 can be used to control physicalcharacteristics of the node connection port 2, such as the degree ofmovement in the bond element. This actuation can be based on informationprovided by the virtual model, discussed in more detail below. Acommunication interface 6 can exchange data with other node elements 1using the physical connection with a bond element.

The node element 1 can be used to assemble a plurality of structuralelements, including other node elements and bond elements 3. The nodeelement can be combined with an adjacent structural element, such as abond element, to form a structural assembly corresponding to at least aportion of a physical model.

A computational device 7, such as a microprocessor, can be embedded inthe node element. The computational device can be connected, wirelessly,wired, or otherwise, to an energy supply 8 (such as a battery), a memorydevice 9, a communications device 10, the node connection port 2, asensor 4, and/or a control device 5. A computational unit can be usedthat includes both the computational device 7 and the memory device 9.The energy supply 8 can be located within a node element 1 and cansupply power to the functional elements and embedded systems.Embodiments include external power sources, e.g., such that power can betransmitted to a node element through a connection port. The memorydevice contains the embedded rules of the physical model (e.g., anatomic unit) and operational instructions for the functioning of thenode element. Such instructions can include, e.g., actuation informationfor control device 5. In some embodiments, the memory device can storeunique characteristics of the node element 1, input data from thecommunications device 10, output for a transmission device,communication rules for determining the state of a physical model, basicrules for physical model building, and computational functions for theprocessing the instructions and interpreting the rules. The computationdevice 7 can control the state of the node element, i.e., interactionswith connection port 2, sensor 4, control device 5, communicationprocesses, error correction, and/or maintenance of the system.

The communication device 10 can be connected to the computational device7 to receive or transmit data with other structural elements such asnode elements or bond elements, and with the virtual model orcomputer-based visualization and simulation software tools running,e.g., on an external computer system. These communications can betransmitted by wire, wirelessly, or by other means known to the skilledartisan.

A bond element 3 can represent an atomic, ionic, molecular, or covalentconnection or bond, and is preferably rod-shaped. Each bond element canhave two bond connection ports 11, disposed at each end of the bondelement. Each of these can physically couple with a node connection port2, and can also include sensors. The types of sensors used with the nodeelement can also be used with bond elements. In some embodiments a bondinterface port 13 can facilitate communications with a node elementthrough node connection port 2. In other embodiments the bond element 3can include a bond communicator 12 comprising memory, computational, andcommunications functions. In this respect a bond communicator 12 issomewhat similar to the computational unit of the node element, and insome embodiments can perform the functions of the computational unit fora node element. The bond communicator 12 can store the identity or othercharacteristics (e.g., physical characteristics) of the particular bond.In some embodiments the bond element includes a physical communicationcapability allowing the exchange of information between the bond elementand a node element, or facilitating the exchange of information betweendifferent node elements. Thus, the bond communicator 12 can perform manyof the functions ascribed to the computational unit (e.g., thecomputational device 7) of the node element 1, thereby providing arobust, distributed, and potentially redundant computationalconfiguration. In some embodiments the computational capability of thebond communicator is used to meet other computation requirements of themodel, e.g., compensating for node elements that do not have acomputational device 7.

FIGS. 4A and 4B are exemplary diagrams illustrating the construction ofa simple physical model. A node element 1 can be coupled with bondelement 3, e.g., by physically connecting the parts as illustrated inFIGS. 4A and 4B. Elements and embedded devices such as these can becombined to create an intelligent physical molecular model thatrepresents a single simple molecule 14, as illustrated in FIG. 5. Withadditional node elements 1 and bond elements 3, a more complex physicalmodel can be created that represents a complex molecular structure, suchas is illustrated in FIG. 6. FIG. 6 is merely a two-dimensionalrepresentation of what could be a very complex three-dimensional model.The physical characteristics of the molecular model can represent,simulate, and be used to predict, for example, physical characteristicssuch as the rotatable bonds 17 and the bendable angels 18 of the model,which are illustrated in FIG. 7.

In some embodiments the computation and communication requirements of aplurality of node elements of the physical model can be consolidated onto one node element that has information of constituent nodes and bondswithin certain boundaries, such as within a molecule (i.e., in amolecular modeling context). In such an embodiment, use of passiveelements (i.e., node or bond elements that do not include acomputational unit or a bond communicator, respectively) obviates theneed to install expensive computational and communication functionalityin each element.

From the above it can be understood that many different embodiments of aphysical model can be assembled from individual structural elements suchas node elements and bond elements. The assembled structure possessescertain physical characteristics imparted to it at least in part by itsphysical configuration, some of which are detected and stored by thesensors 4 and other functional elements of the model. Information ofthese physical characteristics can then be transmitted to a virtualmodel, such as a simulation software tool operating on a computer 21, bymeans of a wired, wireless or other communications system(s).

The information of physical characteristics of the physical model ispreferably provided to a virtual model operating on a computer system.Physical models created with node and bond elements, e.g., representingatomic units with imbedded knowledge and interconnectivity, can bemanipulated in three-dimensional space in real time. The informationthus created can be provided to a computer system external to thephysical model, whereby complex calculations, predictions, and variouscomputationally intensive modeling results can be generated and used.

The virtual modeling software can consist of visualization tools andsimulation tools. A visualization software tool allows representation ofthe various characteristics of the physical model on a visualizationplatform, such as a computer screen. A simulation software tool can beused to represent and convey additional characteristics such asenergetics, quantum mechanical effects, vibrational modes, crystallattice construction, molecular dynamics and other characteristics notvisible to the human eye. The simulation software tools also allow forthe control or calculation of such characteristics by means ofparameters or inputs supplied by the physical model, various softwaretools, the user, and/or various testing devices.

A user can modify input variables of the virtual model, displayparameters of the molecular structure, and even create a movie of all orpart of the molecular structure, or its simulation, with the click of abutton. Various rendering options can also be used to create pictures ofvarious sizes and resolutions. Such images can be posted on theInternet, or they can be of sufficient resolution to create a largeposter.

FIG. 1, discussed above, illustrates a communications device 10 used toexchange information between the physical model and the virtual model ofthe computer-based software tool. The communications device 10 canprovide the connectivity required by the hybrid modeling system, and iscapable of transmitting the basic molecular geometry of the physicalmodel to the virtual model, of the virtual model to the physical model,or both. In a preferred embodiment, such communications are performedwirelessly between one or more node elements 1 of the physical model anda peripheral communications device such as an 802.11B wireless port of acomputer system (not shown). The information provided to the virtualmodel allows a set of molecular coordinates to be determined anddisplayed on a display device, such as a computer screen. Using thisinformation, a simulation software tool can represent molecularcharacteristics such as energetics, quantum mechanical effects,vibrational modes, crystal lattice construction, and molecular dynamicsand other characteristics not visible to the human eye. The user canalso impose certain changes or restrictions through the software toolsthat can be displayed visually or represented in the physical model.

Moreover, embodiments include providing information of virtualcharacteristics from the virtual model to the physical model, such thatphysical characteristics are created or actuated on the physical model.Such characteristics can be represented, e.g., by LED's, vibratingunits, or other suitable means. Such communications can bebi-directional. For example, physical actuation of an LED, a vibratingunit, switches, and the like on the physical model can be associatedwith desired virtual characteristics of the virtual model. Of course, auser can also modify the virtual model by adding or removing nodeelement 1 (e.g., atoms) in the physical model. Manipulation ofconnections, rotational orientations, dihedral angles, and the like canalso be used to modify attributes of the virtual model, by physicallychanging the physical model. In a preferred embodiment, suchmodifications and changes to the physical model can be updated in thevirtual model in real-time. Thus, as the user modifies the physicalmodel, those results are relayed to the virtual model where they aredisplayed, and can be used as input for a modeling software tool.

Characteristics of the physical model (e.g., physical characteristics)and characteristics of the virtual model (e.g., virtual characteristics)thus become somewhat intertwined using the hybrid model of theinvention. An LED or some other type of display device can be used torepresent on the physical model a virtual characteristic from thevirtual model that would ordinarily not easily be physically displayedor be a part of a physical model. The converse relationship can also beestablished, wherein a device on a structural element of the physicalmodel can be provided or manipulated by a user to represent a virtualcharacteristic, and information of or from this physical representationcan be provided to the virtual model for computational or graphicaldisplay purposes. Distinctions between physical characteristics andvirtual characteristics thus become blurred. Accordingly, if desired,each of the physical and virtual characteristics described herein can berepresented in some form on the physical model, and can also berepresented within and by the virtual model. In addition to physicalcharacteristics and virtual characteristics described elsewhere in thisdocument, such characteristics can also include positional information,relative and absolute movement of model elements (e.g., structuralelements), physical pressure and/or stress on and within the modelelements, the size of a node element (e.g., an atom) or a bond elementsuch that the larger node element (e.g., carbon) is distinguished fromthe smaller node element (e.g., hydrogen), or a bond elementrepresenting a certain strength or type (e.g., a single bond) can bedistinguished from a bond element of a different strength or type (e.g.,a double bond).

When the computer-based virtual model is used to communicate with thephysical model (e.g., when the invention is used as a molecular model),certain molecular rules can be imposed on the construction, or physicalresponse, of the physical model through the software tools that residein the computer system of the virtual model, the computational unit ofthe node element, and/or the bond communicator of the bond elements.Thus, a mechanism can be established that exchanges information from thephysical model to the virtual model as it is visualized or simulated inthe computer. Further, certain rules and new parameters can be imposedon the embedded atomic elements, such that the models can be modified asknowledge of molecular characteristics advances. In situations whereexperimental modeling results are desired, this process can beiterative.

Other embodiments include a feedback loop, where information isexchanged in both directions between the physical model and the virtualmodel. For example, when a control device 5 implements on the physicalmodel the results of experimental virtual modeling, a user can modify orupdate the physical model. Such manipulation can then be detected by thephysical model, as described above, and information of the updatedphysical characteristics can be provided to the virtual model. Anotheriteration of the modeling results can then be performed. This methodprovides to the user the benefits of both physical and virtual modelsand modeling techniques, while increasing efficiency and productivity.

Embodiments include a communications interface that can determine therelative location of node elements in three-dimensional space, e.g.,through use of a GPS system that utilizes a position indicator, such asa beacon, at the center or on the surface of a the node element. Asensor can be provided that triangulates the position of the positionindicator relative to other node elements.

The physical modeling tool and the virtual modeling tool, combined withthe use of other software tools, can be used independently of each otherat particular times, but can later be interconnected with each other.For example, a person can visit a potential customer with a physicalmodel, and later upload information from the physical model to thecustomer's visualization or simulation software, thereby demonstratingcertain characteristics that would not be obvious to the unaided humaneye or intellect simply by observing the physical model.

The invention can also be used in both the classroom and researchlaboratory environments. For example, high school students currentlyusing static, unintelligent models can use the invention to learn aboutthe dynamic characteristics of physical (e.g., molecular) structures.Commercial researchers can use the invention to gain meaningful insightsinto the complex relationships on the atomic level, and to representsuch relationships in both physical and virtual formats.

It should be understood that the invention is not limited by theforegoing description, but embraces possible such alterations,modifications, and variations.

By the above it can be seen that a highly useful apparatus and methodshave been developed for creating and interconnecting various physicaland virtual models, whereby considerable time savings and efficiencyimprovements can be obtained. The terms and expressions employed hereinare used as terms of description and not of limitation, and there is nointention, in the use of such terms and expressions, of excluding anyequivalents of the features shown and described or portions thereof, butit is recognized that various modifications are possible within thescope of the invention claimed.

1. A node element for use in assembling a plurality of structuralelements comprising: a body; one or more connection ports disposedrelative to the body, at least one connection port capable of beingcoupled to an adjacent structural element; and a computational unitdisposed within the body, wherein the computational unit receivesinformation of physical characteristics of the node element from theconnection port.
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